Among other data, *.cif include the position of the (hopefully correctly assigned) atoms, but nothing about hybridization ($sp^3$, $sp^2$. This is why representing organometallic complexes (like ferrocenes) drawn in sight of what is important for a crystallographer may differ from the one drawn by an organo(metallic) chemist. To annotate our structure, let's label the residues and label the inhibitor, a drug called Atazanavir.The current definition of the *.cif file does not care about bond order, rather than indicating connectivity of atoms within a molecule. To provide these for the user automatically, let's clear the measurements then apply them programmatically.
Double-click on the inhibitor's hydroxyl again, then move the mouse to the oxygen atom on the other Asp residue at a distance of 0.257 nanometers. Double-click on DR7's hydroxyl group, then move the mouse to the Asp oxygen atom 0.257 nanometers away, and double-click again. To show that the interaction makes sense geometrically, let's measure the smallest distance between the Asp residues and the inhibitor's hydroxyl group. Finally, let's move the display to a convenient location. The ligand's hydroxyl group is the key group, so let's remove extraneous atoms from the ligand to focus on the key interaction. Let's color and resize the amino acid side chains to distinguish them from the ligand-Jmol understands several different color schemes for proteins. With the key subset in place, we can now think separately about the ligand and the protein. Load it up later by pasting the text into the Console.
If you're worried about messing up your structure while executing a command, use the write state command to save your work! Copy the output of write state to a text file to save the appearance of your Jmol. We can restore the default selecting behavior by subsetting the entire structure (avoid doing this for now).īe careful! Jmol commands are irreversible. Notice that only the bonds in our subset are altered, even though the select command we used was "select all"! With the subset confirmed, let's widen the bonds again. For visual conformation, let's select the subset and make bonds thinner. To simplify future commands, let's subset the currently displayed atoms so that no commands extend beyond the scope of these atoms. Hover your mouse over an atom to see its atom number and what built-in atom group it belongs to (a three-letter abbreviation in brackets).įrom here on out we would only like to work with this atom set. Can you see what we've done? Only the DR7 inhibitor and two amino acid residues are now displayed in the Jmol window. To zoom in on the display, Shift-click and drag on the Jmol window.
After reading a reference and exploring the 2FXD structure on the Protein Data Bank, let's imagine we learned that the ligand exhibits two hydrogen bonds with two aspartic acid side chains on the protein.įirst, let's select and hide the entire structure, then select and display only what we need. The Jmol at right is a complex of an HIV reverse transcriptase with an inhibitor-but you wouldn't know it from the view shown! Let's clean this structure up to highlight the role of the ligand and how it interacts with the protein. To do this, you will often have to "whittle" structures down to their essential components. We would like you to distill the behavior and properties of macromolecular assemblies to the level of "bonds and atoms" we explore in CHEM 332.
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